Which ones can stand along with The City on the Edge of Forever, or The Inner Light?

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None of them are really at that level, sorry.

I'd say the essential episodes are:

Caretaker
State of Flux
Faces
Jetrel
Lifesigns
Deadlock
The Thaw
Tuvix
Before and After
Scorpion
The Gift
The Raven
Year of Hell
Living Witness
Infinite Regress
Counterpoint
Relativity
Pathfinder
Blink of an Eye
Collective
Child's Play
Life Line
Muse
Critical Care
Inside Man
Lineage
The Void
Author, Author
Homestead
Endgame